Characterization of Bacterial Communities in Air and Bedding Materials of Intensive Donkey Farms During Summer

This study investigated the bacterial community composition and diversity in air and exercise yard bedding samples from large-scale donkey farms in Liaocheng, China, during summer using 16S rRNA high-throughput sequencing. Air samples were collected from five functional areas of donkey barns, while bedding samples were obtained from eight farms housing Dezhou donkeys. Sequencing analysis revealed 894 operational taxonomic units (OTUs) in air samples and 3127 OTUs in bedding samples. Alpha diversity indices indicated that the mare barn exhibited the highest microbial diversity in air, while the foal barn showed the lowest. <i>Actinobacteriota</i>, <i>Proteobacteria</i>, and <i>Firmicutes</i> were the dominant phyla across different functional areas. <i>Rhodococcus</i> was identified as the predominant airborne genus, representing a potential pneumonia risk in foals. In bedding materials, <i>Firmicutes</i>, <i>Actinobacteriota</i>, and <i>Proteobacteria</i> predominated, with <i>Corynebacterium</i>, <i>Salinicoccus</i>, and <i>Solibacillus</i> as dominant genera. Several potentially pathogenic bacteria were detected, including <i>Rhodococcus</i>, <i>Corynebacterium</i>, <i>Clostridium</i>, <i>Streptococcus</i>, and <i>Escherichia-Shigella.</i> These findings provide critical insights into the microbial ecology of intensive donkey farming environments and offer scientific evidence for developing targeted biosecurity strategies to safeguard animal health and promote sustainable livestock production.